Citation: | LI Zhibo, DONG Shiman, LI Shuxia, et al. Identification and expression of SR45 subfamily gene in Manihot esculenta[J]. Journal of South China Agricultural University, 2022, 43(5): 20-28. DOI: 10.7671/j.issn.1001-411X.202111032 |
As major members of the splicing complex, arginine/serine-rich proteins (SR) not only participate in the process of alternative splicing of plant precursor mRNA, but also play an important role in abiotic stress. SR45 gene is a member of SR gene subfamily, this study was aimed to analyze the structural characteristics and expression patterns of SR45 subfamily proteins in cassava, and provide a theoretical support for further understanding the functions of SR45 subfamily genes in cassava.
The evolutionary tree of cassava SR gene family was reconstructed by bioinformatics, and the physical and chemical properties, gene structure and conserved domain of cassava SR45 subfamily protein were analyzed. At the same time, transcriptome data were used to analyze the changes of SR gene expression under low temperature and drought stress, quantitative real-time PCR (RT-qPCR) was used to study the specific expression of SR gene members in different tissues and their responses to low temperature stress.
The cassava SR gene family consisted of 26 members in seven categories, and the SR45 subfamily consisted of five members. The length of proteins encoded by SR45 subfamily genes were 135–417 aa, with relative molecular mass being 14970–47210, PI being 5.19–12.34. It was predicted that they were mainly located in the nucleus and chloroplast. The RS domain and RRM domain encoded by SR45 had Motif 3, Motif 6, Motif 2 and Motif 1 conserved motifs. Transcriptional data and RT-qPCR analysis showed that all SR45 genes were responsive to low temperature stress in cassava, MeSR45-2 was significantly up-regulated, MeSR45-4and MeSR45-5 were highly expressed in roots and leaves of cassava.
SR45 subfamily genes of cassava significantly respond to low temperature stress. MESR45-2 gene is selected as the candidate gene for regulating low temperature stress, root and leaf are the main tissues for SR45 subfamily gene research. This study lays a theoretical foundation for the exploration of cassava SR45 gene, and points out a direction for further research on cassava SR45 gene responsive to stress.
[1] |
COCK J H. Cassava: A basic energy source in the tropics[J]. Science, 1982, 218(4574): 755-762. doi: 10.1126/science.7134971
|
[2] |
HUANG L, YE Z, BELL R W, et al. Boron nutrition and chilling tolerance of warm climate crop species[J]. Annals of Botany, 2005, 96(5): 755-767. doi: 10.1093/aob/mci228
|
[3] |
LEVIATAN N, ALKAN N, LESHKOWITZ D, et al. Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana with tiling microarray[J]. PLoS One, 2013, 8(6): e66511. doi: 10.1371/journal.pone.0066511
|
[4] |
SHEN Y F, WU X P, LIU D M, et al. Cold-dependent alternative splicing of a Jumonji C domain-containing gene MtJMJC5 in Medicago truncatula[J]. Biochemical and Biophysical Research Communications, 2016, 474(2): 271-276. doi: 10.1016/j.bbrc.2016.04.062
|
[5] |
IIDA K, SEKI M, SAKURAI T, et al. Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences[J]. Nucleic Acids Research, 2004, 32(17): 5096-5103. doi: 10.1093/nar/gkh845
|
[6] |
THATCHER S R, DANILEVSKAYA O N, MENG X, et al. Genome-wide analysis of alternative splicing during development and drought stress in maize[J]. Plant Physiology, 2016, 170(1): 586-599. doi: 10.1104/pp.15.01267
|
[7] |
LIU Z S, QIN J X, TIAN X J, et al. Global profiling of alternative splicing landscape responsive to drought, heat and their combination in wheat (Triticum aestivum L.)[J]. Plant Biotechnology Journal, 2018, 16(3): 714-726. doi: 10.1111/pbi.12822
|
[8] |
REDDY A S N, ALI G S. Plant serine/arginine-rich proteins: Roles in precursor messenger RNA splicing, plant development, and stress responses[J]. Wiley Interdisciplinary Reviews: RNA, 2011, 2(6): 875-889. doi: 10.1002/wrna.98
|
[9] |
LI S X, YU X, CHENG Z H, et al. Large-scale analysis of the cassava transcriptome reveals the impact of cold stress on alternative splicing[J]. Journal of Experimental Botany, 2020, 71(1): 422-434.
|
[10] |
LI Y, GUO Q, LIU P, et al. Dual roles of the serine/arginine-rich splicing factor SR45a in promoting and interacting with nuclear cap-binding complex to modulate the salt-stress response in Arabidopsis[J]. New Phytologist, 2021, 230(2): 641-655. doi: 10.1111/nph.17175
|
[11] |
PALUSA S G, ALI G S, REDDY A S N. Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins: Regulation by hormones and stresses[J]. Plant Journal, 2007, 49(6): 1091-1107. doi: 10.1111/j.1365-313X.2006.03020.x
|
[12] |
CARVALHO R F, CARVALHO S D, DUQUE P. The plant-specific SR45 protein negatively regulates glucose and ABA signaling during early seedling development in Arabidopsis[J]. Plant Physiology, 2010, 154(2): 772-783. doi: 10.1104/pp.110.155523
|
[13] |
PANDIT S, ZHOU Y, SHIUE L, et al. Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing[J]. Molecular Cell, 2013, 50(2): 223-235. doi: 10.1016/j.molcel.2013.03.001
|
[14] |
BARTA A, KALYNA M, LORKOVIC Z J. Plant SR proteins and their functions[J]. Nuclear Pre-mRNA Processing in Plants, 2008, 326: 83-102.
|
[15] |
BARTA A, KALYNA M, REDDY A S. Implementing a rational and consistent nomenclature for serine/arginine-rich protein splicing factors (SR proteins) in plants[J]. Plant Cell, 2010, 22(9): 2926-2929. doi: 10.1105/tpc.110.078352
|
[16] |
CHEN S, LI J, LIU Y, et al. Genome-wide analysis of serine/arginine-rich protein family in wheat and Brachypodium distachyon[J]. Plants, 2019, 8(7): 188. doi: 10.3390/plants8070188.
|
[17] |
KALYNA M, BARTA A. A plethora of plant serine/arginine-rich proteins: Redundancy or evolution of novel gene functions?[J]. Biochemical Society Transactions, 2004, 32: 561-564. doi: 10.1042/BST0320561
|
[18] |
GU J, MA S, ZHANG Y, et al. Genome-wide identification of cassava serine/arginine-rich proteins: Insights into alternative splicing of pre-mRNAs and response to abiotic stress[J]. Plant and Cell Physiology, 2020, 61(1): 178-191. doi: 10.1093/pcp/pcz190
|
[19] |
马思雅. 木薯SR蛋白家族的系统命名及表达分析[D]. 海口: 海南大学, 2018.
|
[20] |
ZHAO C, ZAYED O, ZENG F, et al. Arabinose biosynthesis is critical for salt stress tolerance in Arabidopsis[J]. New Phytologist, 2019, 224(1): 274-290. doi: 10.1111/nph.15867
|
[21] |
顾进宝. 编码木薯SR蛋白基因的选择性剪接及其调控拟南芥盐胁迫响应中的作用研究[D]. 合肥: 合肥工业大学, 2020.
|
[22] |
ALBAQAMI M, LALUK K, REDDY A S N. The Arabidopsis splicing regulator SR45 confers salt tolerance in a splice isoform-dependent manner[J]. Plant Molecular Biology, 2019, 100(4/5): 379-390.
|
[23] |
CRUZ T M D, CARVALHO R F, RICHARDSON D N, et al. Abscisic acid (ABA) regulation of Arabidopsis SR protein gene expression[J]. International Journal of Molecular Sciences, 2014, 15(10): 17541-17564. doi: 10.3390/ijms151017541
|
[24] |
DAY I S, GOLOVKIN M, PALUSA S G, et al. Interactions of SR45, an SR-like protein, with spliceosomal proteins and an intronic sequence: Insights into regulated splicing[J]. Plant Journal, 2012, 71(6): 936-947. doi: 10.1111/j.1365-313X.2012.05042.x
|
[25] |
ALI G S, PALUSA S G, GOLOVKIN M, et al. Regulation of plant developmental processes by a novel splicing factor[J]. PLoS One, 2007, 2(5): e471. doi: 10.1371/journal.pone.0000471
|
[26] |
ZHANG X N, MOUNT S M. Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development[J]. Plant Physiology, 2009, 150(3): 1450-1458. doi: 10.1104/pp.109.138180
|
[27] |
PARK H J, YOU Y N, LEE A, et al. OsFKBP20-1b interacts with the splicing factor OsSR45 and participates in the environmental stress response at the post-transcriptional level in rice[J]. Plant Journal, 2020, 102(5): 992-1007. doi: 10.1111/tpj.14682
|
[28] |
TANABE N, KIMURA A, YOSHIMURA K, et al. Plant-specific SR-related protein atSR45a interacts with spliceosomal proteins in plant nucleus[J]. Plant Molecular Biology, 2009, 70(3): 241-252. doi: 10.1007/s11103-009-9469-y
|
[29] |
XING D, WANG Y, HAMILTON M, et al. Transcriptome-wide identification of RNA targets of Arabidopsis serine/arginine-rich45 uncovers the unexpected roles of this RNA binding protein in RNA processing[J]. Plant cell, 2015, 27(12): 3294-3308. doi: 10.1105/tpc.15.00641
|
[30] |
XIAO J, HU R, GU T, et al. Genome-wide identification and expression profiling of trihelix gene family under abiotic stresses in wheat[J]. BMC Genomics, 2019, 20: 287. doi: 10.1186/s12864-019-5632-2.
|
[1] | WU Liji, HU Fei. Rainfall characteristics of growth duration of early and late rice in South China[J]. Journal of South China Agricultural University, 2019, 40(1): 1-7. DOI: 10.7671/j.issn.1001-411X.201804034 |
[2] | ZHOU Duo'en, LIU Dewu, LIAO Yingxin, LIU Guangbin. Study on adaptabilities of Hu sheep and Chuanzhong black goat in Southern China[J]. Journal of South China Agricultural University, 2016, 37(5): 19-23. DOI: 10.7671/j.issn.1001-411X.2016.05.004 |
[3] | CHENG Yanbo, MA Qibin, MU Yinghui, TAN Zhiyuan, WU Hong, NIAN Hai. Resistance evaluation of soybean varieties to phytophthora root rot in South China[J]. Journal of South China Agricultural University, 2015, 36(4): 69-75. DOI: 10.7671/j.issn.1001-411X.2015.04.013 |
[4] | ZHAO Yunyun, ZHONG Caixia, FANG Xiaolong, HUANG Yi’an, MA Qibin, NIAN Hai, YANG Cunyi. Genotypic differences of cadmium tolerance among spring-sowing soybean varieties in South China[J]. Journal of South China Agricultural University, 2014, 35(3): 111-113. DOI: 10.7671/j.issn.1001-411X.2014.03.020 |
[5] | LIU Chuan-guang, ZHOU Xin-qiao, CHEN Da-gang, ZHOU Han-qin, FENG Dao-ji, LI Li-jun, LI Ju-chang, ZHANG Gui-quan, CHEN You-ding. Analysis of Coefficient of Parentage Among Major Commercial Inbred Indica Rice Cultivars in South China[J]. Journal of South China Agricultural University, 2012, 33(3): 277-281. DOI: 10.7671/j.issn.1001-411X.2012.03.002 |
[6] | ZHANG Yu-ping,ZENG Ling,LU Yong-yue,LIANG Guang-wen. Monitoring of Insecticide Resistance of Bactrocera dorsalis Adults in South China[J]. Journal of South China Agricultural University, 2007, 28(3): 20-23. DOI: 10.7671/j.issn.1001-411X.2007.03.005 |
[7] | Journal of South China Agricultural University[J]. Journal of South China Agricultural University, 2006, 27(4): F0003-F0003. |
[8] | Cloning and Sequencing of HN Gene of NDV WS99 Strain Isolated in South China[J]. Journal of South China Agricultural University, 2001, 22(4): 75-77. DOI: 10.7671/j.issn.1001-411X.2001.04.021 |
[9] | XIAO Hong-sheng,JI Xian-hua,ZHAO Yu-guang,LUO Fu-he,CHEN Yi-gang. The Application of GPS in South China Forest[J]. Journal of South China Agricultural University, 2000, (2): 5-7. DOI: 10.7671/j.issn.1001-411X.2000.02.002 |
[10] | Wu Zhimin ,Huang Shaowei ,Li Bingtao ,Luo Fuhe. STUDY ON NUMERICAL TAXONOMY OF ULMACEAE PLANTS FROM SOUTH CHINA[J]. Journal of South China Agricultural University, 1995, (3): 51-55. |
1. |
李旭,孙文松,刘莹,杨正书. 北五味子有效成分含量与土壤因子的相关性分析. 园艺与种苗. 2024(01): 68-71 .
![]() | |
2. |
郭城峰,曲娜,吕丽娟. 防风种子不同部位浸提液对白菜种子发芽及幼苗生长的影响. 种子科技. 2024(09): 39-42 .
![]() | |
3. |
马丙如,崔静轩,王雨懿,刘子君,宁凝,王云贺,杨利民,韩忠明. 防风药材质量的多指标综合评价. 浙江农林大学学报. 2024(04): 715-723 .
![]() | |
4. |
李安辉,吕泽良,韩忠明,韩梅,杨利民. 不同碱性盐处理对防风种子萌发、幼苗生长及其生理特性的影响. 中药材. 2023(08): 1870-1875 .
![]() | |
5. |
郝佳,刘宇航,殷洁,刘晶,田新,韩忠明,王云贺,韩梅,杨利民. 不同磷浓度对土壤理化性质及防风生长和药材品质的影响. 华南农业大学学报. 2022(03): 59-67 .
![]() | |
6. |
王浩,秦义杰,钟荣荣,马东来,曾燕,王继永. 基于MaxEnt模型的防风潜在种植区预测. 中国现代中药. 2022(04): 606-610 .
![]() | |
7. |
岳超,徐普,刘柱,施贝,张文婷,王峰. HPLC法同时测定玉屏风口服液中12种成分及质量一致性评价. 中成药. 2022(11): 3434-3439 .
![]() |